Quickstart¶
[1]:
import numpy as np
import matplotlib.pyplot as plt
import ipyvasp as ipv
Transform POSCAR¶
Let’s create some dummy POSCAR.
[2]:
poscar = ipv.POSCAR.new(
[[0.5, 0.5, 0.0], [0.0, 0.5, 0.5], [0.5, 0.0, 0.5]],
{"Ga": [[0.0, 0.0, 0.0]],"As": [[0.25, 0.25, 0.25]]},
scale = 5
)
poscar.write("POSCAR") # need it later
site_kws = dict(alpha=1)
ax1, ax2, ax3 = ipv.get_axes((8,3),ncols=3, axes_3d=[0,1,2])
poscar.splot_lattice( ax = ax1, fill = False,label='original',
site_kws=site_kws)
_ = poscar.transform(lambda a,b,c: (b+c-a, a+c-b, a+b-c)).transpose([1,2,0]) # bring a1 to x
print(poscar.last.data.metadata.TM)
poscar.last.splot_lattice( # .last points to last created POSCAR in transform
ax=ax2, fill = False, color='red', label='transformed',
site_kws=site_kws
)
poscar.last.splot_plane([1,1,0],1/2,ax=ax2)
poscar.transform(lambda a,b,c: (a-c,b-c,a+b+c)
).set_zdir([0,0,1]).splot_lattice(ax=ax3,color='red')
print(poscar.last.data.metadata.TM)
ax1.view_init(azim=-25, elev=15)
ax2.view_init(azim=-35, elev=15)
---------------------------------------------------------------------------
FileExistsError Traceback (most recent call last)
Cell In[2], line 8
1 poscar = ipv.POSCAR.new(
2 [[0.5, 0.5, 0.0], [0.0, 0.5, 0.5], [0.5, 0.0, 0.5]],
3 {"Ga": [[0.0, 0.0, 0.0]],"As": [[0.25, 0.25, 0.25]]},
4
5 scale = 5
6 )
----> 8 poscar.write("POSCAR") # need it later
10 site_kws = dict(alpha=1)
11 ax1, ax2, ax3 = ipv.get_axes((8,3),ncols=3, axes_3d=[0,1,2])
File /opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ipyvasp/lattice.py:736, in POSCAR.write(self, outfile, **kwargs)
733 @_sub_doc(plat.write_poscar)
734 @_sig_kwargs(plat.write_poscar, ("poscar_data",))
735 def write(self, outfile=None, **kwargs):
--> 736 return plat.write_poscar(self.data, outfile=outfile, **kwargs)
File /opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/ipyvasp/_lattice.py:296, in write_poscar(poscar_data, outfile, selective_dynamics, overwrite, comment, scale)
294 f.write(out_str)
295 else:
--> 296 raise FileExistsError(
297 f"{outfile!r} exists, can not overwrite, \nuse overwrite=True if you want to chnage."
298 )
299 else:
300 print(out_str)
FileExistsError: 'POSCAR' exists, can not overwrite,
use overwrite=True if you want to chnage.
[3]:
poscar.splot_bz(fill = True,color='skyblue', vectors=None,lw=0.1).set_axis_off()
ax = poscar.splot_kpath([(0,0,0), (1/4,1/2,-1/4), (0.5,0.5,0), (0,0,0), (0,0.5,0)],
labels = ['Γ', 'K', 'X', 'Γ', 'L'], fmt_label=lambda lab: lab+'\n')
ax.view_init(azim=55, elev=25)
<Figure size 489.6x489.6 with 0 Axes>
[4]:
fig = poscar.iplot_bz(color='blue')
ipv.iplot2html(fig)
[4]:
K-Path¶
We can interplate kpath based on current POSCAR, it gives correct distance between points.
[5]:
poscar.get_kpath([
(0,0,0,'Γ'),
(1/4,1/2,-1/4,'K'),
(0.5,0.5,0,'X'),
(0,0,0,'Γ'),
(0,0.5,0,'L')
], n=8)
Automatically generated using ipyvasp for HSK-PATH 0:Γ, 4:K, 5:X, 9:Γ, 12:L
13
Reciprocal Lattice
0.0000000000 0.0000000000 0.0000000000 0.076923
0.0625000000 0.1250000000 -0.0625000000 0.076923
0.1250000000 0.2500000000 -0.1250000000 0.076923
0.1875000000 0.3750000000 -0.1875000000 0.076923
0.2500000000 0.5000000000 -0.2500000000 0.076923
0.5000000000 0.5000000000 0.0000000000 0.076923
0.3750000000 0.3750000000 0.0000000000 0.076923
0.2500000000 0.2500000000 0.0000000000 0.076923
0.1250000000 0.1250000000 0.0000000000 0.076923
0.0000000000 0.0000000000 0.0000000000 0.076923
0.0000000000 0.1666666667 0.0000000000 0.076923
0.0000000000 0.3333333333 0.0000000000 0.076923
0.0000000000 0.5000000000 0.0000000000 0.076923
[6]:
poscar.get_kmesh(2,2,2, weight=0)
Generated uniform mesh using ipyvasp, GRID-SHAPE = [2,2,2]
8
Reciprocal
0.0000000000 0.0000000000 0.0000000000 0.000000
1.0000000000 0.0000000000 0.0000000000 0.000000
0.0000000000 1.0000000000 0.0000000000 0.000000
1.0000000000 1.0000000000 0.0000000000 0.000000
0.0000000000 0.0000000000 1.0000000000 0.000000
1.0000000000 0.0000000000 1.0000000000 0.000000
0.0000000000 1.0000000000 1.0000000000 0.000000
1.0000000000 1.0000000000 1.0000000000 0.000000
[7]:
view = poscar.view_weas(colors={'Ga':'red','As':'blue'})
view
[7]:
If you are not seeing interactive widget above, don’t worry! We’ve got you covered with a screenshot below:
[8]:
view.download_image('weas.png')
Live View of POSCAR Operations¶
Batch analysis using Files class.¶
[9]:
files = ipv.Files('.')
files
[9]:
Files(
PosixPath('POSCAR'),
PosixPath('quickstart.ipynb'),
PosixPath('weas.png')
) 3 items
[10]:
files.summarize(lambda path: {'end': path.parts[-1]})
[10]:
| end | FILE | |
|---|---|---|
| 0 | POSCAR | POSCAR |
| 1 | quickstart.ipynb | quickstart.ipynb |
| 2 | weas.png | weas.png |
[11]:
files.map(lambda p: p.suffix,to_df=True)
[11]:
| 0 | 1 | |
|---|---|---|
| 0 | POSCAR | |
| 1 | quickstart.ipynb | .ipynb |
| 2 | weas.png | .png |
[12]:
files.interactive(lambda file: print(file))
[12]:
[13]:
files.filtered('py')
[13]:
Files(
PosixPath('quickstart.ipynb')
) 1 items
Example: View Lattice and BZ side by side¶
[14]:
import plotly.graph_objects as go
import ipyvasp as ipv
fs = ipv.Files('.','POSCAR')
@fs.interact(fig1 = go.FigureWidget(), fig2 = go.FigureWidget(),
app_layout={"left_sidebar": ('file', 'fig2'), 'center':('fig1',),'pane_widths':[2,3,0]})
def view(file, fig1, fig2):
pos = ipv.POSCAR(file)
ipv.iplot2widget(pos.iplot_bz(), fig_widget=fig2)
ipv.iplot2widget(pos.iplot_lattice(), fig_widget=fig1)
